Contacts of the helix formed by residues 79 - 90 (chain B) in PDB entry 2HQR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ARG* 3.5 6.0 - - - +
77B ASN* 2.6 43.4 + - - +
78B PRO* 1.3 76.9 - - - +
80B SER* 1.3 63.9 + - - +
81B GLU* 3.0 14.3 + - - +
82B GLU* 3.2 22.5 + - - +
83B GLU* 3.0 21.1 + - - +
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Residues in contact with SER 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ARG* 3.5 19.0 - - - +
101A SER* 3.3 36.1 + - - -
104A ALA* 4.3 7.0 - - - -
79B THR* 1.3 74.0 - - - +
81B GLU* 1.3 70.5 + - - +
83B GLU* 3.6 5.3 - - - +
84B VAL* 3.3 28.5 + - - +
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Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B THR* 3.0 12.7 + - - +
80B SER* 1.3 84.9 - - - +
82B GLU* 1.3 61.1 + - + +
84B VAL* 3.1 13.1 - - - +
85B HIS* 2.4 36.1 + - + +
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 6.0 9.0 - - + +
75B SER* 2.5 35.8 + - - -
77B ASN* 2.9 30.2 + - - +
79B THR* 3.2 15.9 + - - +
81B GLU* 1.3 78.2 - - + +
83B GLU* 1.3 61.1 + - - +
85B HIS* 4.2 6.5 - - - -
86B ALA* 2.8 32.6 + - - +
94B TYR* 4.2 7.5 + - + -
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ARG* 3.9 21.5 + - - +
104A ALA* 4.6 22.0 - - + +
107A ALA* 6.5 0.2 - - + -
108A ARG* 5.5 1.1 - - + +
79B THR 3.0 14.3 + - - +
80B SER* 3.6 11.2 - - - +
81B GLU 3.2 0.2 - - - -
82B GLU* 1.3 80.9 - - - +
84B VAL* 1.3 64.3 + - + +
86B ALA* 3.3 7.3 + - - +
87B PHE* 3.3 48.6 + - + -
94B TYR* 3.2 33.0 - - - +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS* 5.1 5.8 - - + +
104A ALA* 4.6 13.7 - - - +
107A ALA* 4.3 24.2 - - + -
80B SER* 3.3 13.4 + - - +
81B GLU* 3.1 17.5 - - - +
83B GLU* 1.3 75.0 - - + +
85B HIS* 1.3 71.2 + - + +
87B PHE* 3.4 4.4 + - - -
88B GLU* 2.7 43.7 + - + +
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Residues in contact with HIS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 3.8 24.5 - - + -
81B GLU* 2.4 38.9 + - + +
82B GLU* 3.8 6.3 - - - +
84B VAL* 1.3 91.6 - - + +
86B ALA* 1.3 58.1 + - - +
88B GLU* 4.2 4.9 - - + -
89B GLN* 2.7 52.1 + - + +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 5.3 7.5 - - + +
73B VAL* 4.4 6.7 - - + -
82B GLU 2.8 18.6 + - - +
83B GLU* 3.6 6.1 - - - +
84B VAL 3.2 0.2 - - - -
85B HIS* 1.3 78.7 - - - +
87B PHE* 1.3 63.9 + - + +
89B GLN* 4.5 1.7 - - - +
90B GLY 3.3 4.9 + - - -
91B ALA* 2.8 43.7 + - + +
94B TYR* 4.3 21.8 - - + -
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Residues in contact with PHE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ASP* 6.0 0.4 - - - -
104A ALA 6.0 0.2 - - - -
107A ALA* 5.6 5.4 - - + +
108A ARG* 2.8 66.2 - - + -
111A ALA* 4.7 17.2 - - + +
83B GLU* 3.3 50.4 + - + +
84B VAL* 4.1 3.6 - - - +
86B ALA* 1.3 81.7 - - + +
88B GLU* 1.3 69.7 + - + +
90B GLY* 3.8 7.8 + - - -
91B ALA* 3.8 22.1 + - + +
92B ASP 4.0 10.1 - - - -
93B ASP* 4.9 7.9 - - - -
94B TYR* 5.1 6.7 - - + -
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ALA* 5.8 4.4 - - + +
84B VAL* 2.7 40.9 + - + +
85B HIS* 4.2 5.6 - - + +
87B PHE* 1.3 75.4 - - + +
89B GLN* 1.3 69.4 + - + +
90B GLY* 4.5 0.2 - - - -
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Residues in contact with GLN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 3.8 44.4 - - + +
59B VAL* 4.5 8.7 - - + -
60B SER* 4.4 22.0 + - - -
63B LYS* 4.9 3.1 - - - +
85B HIS* 2.7 47.1 + - + +
86B ALA* 4.5 1.3 - - - +
88B GLU* 1.3 77.9 - - - +
90B GLY* 1.3 56.0 + - - +
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Residues in contact with GLY 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B VAL* 3.5 16.8 - - - +
63B LYS* 3.0 42.1 - - - +
71B VAL* 4.4 1.7 - - - +
86B ALA 3.3 3.4 + - - -
87B PHE 4.2 4.9 - - - -
88B GLU 3.4 1.6 - - - -
89B GLN* 1.3 81.7 - - - +
91B ALA* 1.3 60.4 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il